'Super' El Nino: Why 1.5m Kenyans could face floods

At least 1.5 million Kenyans could be adversely affected by flooding during the October-December rainfall season, with several counties facing the risk of displacement, destruction of farms, infrastructure, and loss of lives .

Tana River, Garissa, Kilifi, Mandera, Marsabit, Wajir, Nairobi, Busia, Kisumu, Narok, Mombasa and Baringo Counties will be hit the hardest with devastating impacts.

A further estimated 450,000 households will also be exposed to landslides in prone counties including Murang’a, Elgeyo Marakwet, West Pokot, Kiambu, Baringo, Makueni and Tharaka Nithi counties, where consecutive days of rainfall of between 20mm and 50mm a day are expected.

The prolonged rains will also lead to disease outbreaks with another 1.5 million households being exposed to vector and waterborne diseases in the North Eastern, Coastal and Lake Basin regions.

This emerged during the 74th Greater Horn of Africa Climate Outlook Forum in Kigali, Rwanda.

According to a forecast by the IGAD Climate Prediction and Applications Center (ICPAC) the forecast of very heavy rainfall in Kenya and the Greater Horn of Africa as a result of a Very Strong El Niño and a strong positive Indian Ocean Dipole (IOD).

El Niño is a climate phenomenon that alters temperature and rainfall patterns in different parts of the world.

In the East Africa region, the impact of El Niño is influenced by other climate drivers, including the Indian Ocean Dipole.

The IOD refers to differences in sea surface temperatures between the western and eastern Indian Ocean. A positive IOD occurs when waters in the western Indian Ocean, including those near the east African coast, are warmer while waters towards Australia are cooler.

According to the forecast, there is more than a 75 per cent probability of a positive IOD and a 96 per cent chance of a very strong El Nino during the October-November-December rainfall season.

"What we are expecting in 2026 is a very strong El Niño, with over 90% probability that this could be a very, very strong El Nino. we are also seeing over 75% probability that we'll be having a positive Indian Ocean Dipole, which is currently neutral, but expected to fall into the positive phase any time from now," said Hannah Kimani from Kenya Meteorological Services.

The heavy rainfall is expected to affect most countries in the IGAD region, including Kenya, Uganda, Somalia, Ethiopia, South Sudan and Tanzania.

Regionally, the forecast shows that North Eastern Kenya, Central to Southern Somalia and South Eastern Ethiopia will experience above-average rainfall.

Some regions are likely to receive upto 500 millimeters of rainfall depending on the strength of the positive IOD.

In Western and Eastern parts of the region, experts warned that there’s over 90 percent chance of rainfall exceeding 300mm.

The regional forecast also indicates that parts of the Greater Horn could receive more than 500 millimetres during the season, while some areas including parts of Rwanda, Burundi, and Lake Victoria Regions in Kenya, Tanzania and Uganda will experience prolonged wet spells lasting between 10 and 15 consecutive days.

Southern Ethiopia, Somalia and cross-border areas of Kenya, Uganda, and South Sudan are expected to experience maximum of 8 to 10 dry days.

High-ground areas will be vulnerable to landslides, while low-lying areas are expected to face greater flood risks. Urban areas like Nairobi could also face pressure from heavy rainfall if drainage systems cannot cope with the volume of water.

However, areas in the Western region is expected to have a delayed onset, while early onset is expected in the eastern and southern parts.

"There are some areas that are high ground, and those are likely to be prone to things we call landslides.Others are low lying, and those are the areas that are likely to experience maybe what you would call massive flooding, and also the urban centers," said kimani.

While much of the equatorial Greater Horn is expected to receive enhanced rainfall, some areas, particularly parts of South Sudan, Sudan and other northern parts of the region, could experience comparatively drier conditions.

Despite the heavy rainfall, IPAC indicates that there will be higher-than-average

temperatures across most of the Greater Horn of Africa, with particularly high probabilities in Somalia, Ethiopia and coastal regions.

In Kenya, different regions and sectors will suffer diverse impacts with the agriculture sector, health, pastoralism, and infrastructure being the most vulnerable.

Among the anticipated impacts include floods, dam bursting, destruction of roads and bridges, outbreaks of vector and waterborne diseases including malaria, displacement, deaths, livestock migration, among others.

With the forecast predicting the risk of dams and rivers reaching or exceeding above-normal inflow levels, the experts warned that of increased downstream flooding.

Similarly, the already rising lake levels in Lake Victoria, Turkana and the other lakes in the Rift Valley are expected to rise further, heightening the risks of flooding in the downstream regions and along shorelines, while saturated soils could increase the incidence of landslides.

"This will come with a number of displacements, as people move from higher ground because of those flooding events. Transportation will also be affected as some bridges, roads will be cut off," said Jully Ouma, thematic lead, early warning systems and DRM lead at ICPAC.

According to predictions, the 2026 El Niño could be stronger than previous seasons recorded in the past, including 2023, 2015 and 1997 when a very strong El Niño coincided with a strong positive Indian Ocean Dipole leading to severe rainfall impacts in the country.

The experts warned that rainfall exceeding 30mm a day in urban areas and 50mm a day in rural areas could overwhelm drainage systems, swell rivers and trigger widespread flooding.

However, the rainfall will come in the face of effects of the June-September season, when most areas faced depressed rainfall.

The effect is already being seen in western Kenya and the North Rift, where below-average rainfall has raised concerns over crop performance.

According to Oliver Kipkongei, a regional agrometeorologist at ICPAC, the assessment is particularly worrying for Kenya’s agricultural heartland noting that the North Rift and Western Kenya which form part of the country’s food basket, were affected.

This means that farmers could face a double loss of low yields due low rainfall and post harvest loss causes by the October-December rainfall.

Kenya’s Ministry of Agriculture estimates maize production could be 30 percent or more below normal.

The health sector is expected to suffer a serious crisis during the October-December rainfall season, with a “Super El Niño” scenario expected to bring a combination of flooding and extreme heat, creating conditions favourable for outbreaks of malaria, Rift Valley Fever, cholera, typhoid and other water- and vector-borne diseases, while worsening malnutrition and heat-related illnesses.

The Eastern Africa Scenario-Based Climate-Health Advisories for October-December 2026 cautioned that under the above-normal rainfall scenario, stagnant water by flooding is expected to provide extensive breeding grounds for mosquitoes, potentially driving an increase in malaria, including in highland areas.

The same conditions could fuel Rift Valley Fever, a mosquito-borne viral disease that can affect both livestock and humans.

Flooding would also raise the risk of waterborne diseases like cholera when floodwaters overwhelm latrines and contaminate shallow wells and other water sources.

Children under five are particularly at risk of severe illness and death from diarrhoeal diseases with the health advisories calling for early action, including pre-positioning of diarrhoeal disease and malaria medical supplies, and strengthening disease surveillance at least three weeks before the anticipated peak of flooding.

Crop failures and livestock losses would reduce household access to food, increasing the risk of acute malnutrition with children, pregnant women and breastfeeding mothers expected to be among those most vulnerable.

Women and girls are expected to face gender- and sexual based violence due to their responsibilities involving water collection, food preparation and caregiving.